[Freesurfer] creating custom color table & annotation file

2014-05-16 Thread Maria Jalbrzikowski 
Dear Freesurfer experts,

   I would like to get your help.  I extracted cortical thickness values
from each vertex from each of my individual subjects (example:
path/subject_id/surf/lh.thickness.fsaverage.mgh).
I then ran a covariance analysis over the whole group and identified
"modules" or groups of vertices that covary together.  The modules are
given the names of colors.  I end up with a module (color) assigned to each
vertex.  I now want to visualize this data (so I can if these module
reflect specific neuroanatomical structures), but I'm not sure about how to
do this.  Does anyone know how to do this?  I tried to make a new color
table, with my different module colors as the structures.  I don't know how
to then incorporate this information so that I can view it.  I've read the
tutorials on the label and annotation files, but I have only become more
confused.  If anyone can help me with this problem, I'd be very greatful!

Thank you,

Maria


-- 
Maria Jalbrzikowski, Ph.D.
Department of Psychiatry & Biobehavioral Sciences
University of California, Los Angeles
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[Freesurfer] long_mris_slopes bug

2014-05-16 Thread Katherine Reiter 
Hi Freesurfer experts,

I'm working on analyzing longitudinal data using the longitudinal 2-stage
model. When running the data through long_mris_slopes, I was getting the
following error message: ERROR 1 : mris_calc compute sym. pct. change (spc)
problem?

I saw in previous messages that this is the result of a bug. I found the
fix under the release notes, though after downloading it and placing the
fix in the bin and makign these files executable, I keep receiving the
following error messages. Does anyone have any insight into the problem and
possible solutions?

mri_convert --frame 0 ./tmp-0001_base_lh_thickness_3f8Byr/glm/beta.mgh
./tmp-0001_base_lh_thickness_3f8Byr/beta0.mgh

Traceback (most recent call last):
  File "/Applications/freesurfer//bin/long_mris_slopes", line 744, in

run_cmd(cmd,'mri_convert split frames 0 did not work?')
  File "/Applications/freesurfer//bin/long_mris_slopes", line 422, in
run_cmd
retcode = subprocess.call(args)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 486, in call
return Popen(*popenargs, **kwargs).wait()
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 672, in __init__
errread, errwrite)
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 1202, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error

Thank you,

Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University
Phone: (414) 288-3807
Email: katherine.rei...@marquette.edu
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Re: [Freesurfer] mris_anatomical_stats lgi error

2014-05-16 Thread Marie Schaer 

Hi Andreia,

You probably have lGI values that correspond to earlier versions of your 
surfaces (I.e. maybe you ran lGI first, then did corrections on the surfaces 
and reprocessed them, but forgot to recalculate lGI for this new surfaces).

If you simply reprocess lGI now, that should solve the problem. 

If not let me know,

Marie


On May 16, 2014, at 1:08 PM, "_andre...@sapo.pt" <_andre...@sapo.pt> wrote:

> Hello,
> 
> Only after sending the email below I noticed that now the stats file  
> generated give only 0,00 were the LGI values should be, even though  
> they appear in the terminal.
> 
> How can I solve this issue? And, again, are all the measures (cortical  
> thickness, surface area, aseg) invalidated? As well as qcache? In sum,  
> should I run this subject all from scratch?
> 
> Thank you in advance,
> Andreia Pereira
> 
> 
> Quoting _andre...@sapo.pt:
> 
>> Hi Doug,
>> 
>> I tried to load the annotation and it gave an error. I look in the
>> archives and I found someone with the same problem and the advice was
>> to run:
>> 
>> recon-all -s  -sd  -make all
>> 
>> I did that and tried to run again mris_anatomical_stats as previously
>> and still have this warning
>> 
>> 
>> subj/stats/lh.aparc_lgi.stats subj lh
>> computing statistics for each annotation in aparc.annot.
>> using thickness file pial_lgi.
>> reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
>> reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
>> reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial...
>> reading input white surface  
>> /home/user/visao/Freesurfer//subj/surf/lh.white...
>> MRISreadNewCurvature: incompatible vertex number in file
>> /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
>> No such file or directory
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>> structure is "bankssts"
>> number of vertices  = 1160
>> total surface area  = 813 mm^2
>> total gray matter volume=  0 mm^3
>> average cortical thickness  = 0.000 mm +- 0.000 mm
>> average integrated rectified mean curvature = 0.116
>> average integrated rectified Gaussian curvature = 0.031
>> folding index   = 10
>> intrinsic curvature index   = 1.3
>> structure is "caudalanteriorcingulate"
>> number of vertices  = 810
>> total surface area  = 547 mm^2
>> total gray matter volume=  0 mm^3
>> average cortical thickness  = 0.000 mm +- 0.000 mm
>> average integrated rectified mean curvature = 0.129
>> average integrated rectified Gaussian curvature = 0.034
>> folding index   =  9
>> intrinsic curvature index   = 1.2
>> structure is "caudalmiddlefrontal"
>> number of vertices  = 4752
>> total surface area  = 3134 mm^2
>> total gray matter volume=  0 mm^3
>> average cortical thickness  = 0.000 mm +- 0.000 mm
>> average integrated rectified mean curvature = 0.123
>> average integrated rectified Gaussian curvature = 0.033
>> folding index   = 48
>> intrinsic curvature index   = 6.1
>> structure is "cuneus"
>> number of vertices  = 2701
>> total surface area  = 1667 mm^2
>> total gray matter volume=  0 mm^3
>> average cortical thickness  = 0.000 mm +- 0.000 mm
>> average integrated rectified mean curvature = 0.164
>> average integrated rectified Gaussian curvature = 0.061
>> folding index   = 50
>> intrinsic curvature index   = 7.1
>> 
>> (...)
>> 
>> 
>> The LGI values are generated and they seem to be in the normal range
>> as all the others... I would like to know if this problem invalidates
>> all the other measures that I extracted (cortical thickness and
>> surface area from aparc and Brodmann areas, aseg stats)
>> 
>> Andreia
>> 
>> 
>> Quoting Douglas N Greve :
>> 
>>> That probably means that the subject is out of synch. Try viewing the
>>> subject's surface tksurfer or freeview and load the annotation.
>>> doug
>>> 
>>> On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
 
 Hello all,
 
 I generated the lgi.stats file for all my subjects and in one of them
 I got this warning:
 
 mris_anatomical_stats -a aparc.annot -t pial_lgi -f
 SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
 computing statistics for each annotation in aparc.annot.
 using thickness file pial_lgi.
 reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz...
 reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
 reading input pial surface
 /home/user/visao/Freesurfer//SUBJ/surf/lh.pial...
 reading

[Freesurfer] recon -all with .nii input problems with perl version 5.18

2014-05-16 Thread Samuel Thorpe 

Hello,

I recently upgraded from Ubuntu 13.10 to 14.04, and I started getting a 
new error message while running "recon-all" with .nii file inputs 
(details below). From the error message I believe the problem might be 
that Ubuntu 14.04 ships with perl version 5.18 (as opposed to 5.14 for 
previous versions), and the Ubuntu 14.04 Perl manpage 
(http://manpages.ubuntu.com/manpages/trusty/man1/perl5120delta.1.html), 
specifically lists "shellwords.pl" as a newly deprecated library. 

My naive instinct was to install perl version 5.14 using perlbrew, and 
switch to it whenever a new shell is launched by editing my .bashrc 
file, by adding the lines 
"source ~/perl5/perlbrew/etc/bashrc"

"perlbrew switch perl-5.14.4"

When I do this my shell recognizes perl-5.14.4 as the active version, 
but freesurfer does not. This makes me worry it won't be such a simple 
fix. Any Ideas as to the best way to handle this? Am I on the right 
track?


Many Thanks!
-Samuel Thorpe


bugr related info:
-
FREESURFER_HOME: /usr/local/freesurfer
SUBJECTS_DIR: /usr/local/freesurfer/subjects
"which recon-all" gives "/usr/local/freesurfer/bin/recon-all"
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: jessie/sid
Kernel info: Linux 3.8.0-32-generic x86_64
Linux OS: Ubuntu 14.04 LTS "Trusty Tahr"


example commands executed:
-
subject: "bert", "bert_nii"
after converting "/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz"
to .nii using "mri_convert" (operation successful), I attempt, 
"recon-all -i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s 
bert_nii -all"



error message:
-
"Can't locate shellwords.pl in @INC (@INC contains: 
/usr/local/freesurfer/mni/bin/../lib/mni_autoreg 
/usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl 
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 
/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 
/usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal 
line 460."



/usr/local/freesurfer/subjects/bert_nii/script/recon-all.log attached
Fri May 16 13:00:54 EDT 2014
/usr/local/freesurfer/subjects/bert_nii
/usr/local/freesurfer/bin/recon-all
-i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s bert_nii -all
subjid bert_nii
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux sam-cdl1 3.8.0-32-generic #47-Ubuntu SMP Tue Oct 1 22:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  4096 
memorylocked 64 kbytes
maxproc  256865 
maxlocks unlimited
maxsignal256865 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  328982725213236   27685036  39844 3188042828916
-/+ buffers/cache:2065516   30832756
Swap: 33501180  0   33501180


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/05/16-17:00:54-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: sam  Machine: sam-cdl1  Platform: Linux  PlatformVersion: 3.8.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/05/16-17:00:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: sam  Machine: sam-cdl1  Platform: Linux  PlatformVersion: 3.8.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/05/16-17:00:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: sam  Machine: sam-cdl1  Platform: Linux  PlatformVersion: 3.8.0-32-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/05/16-17:00

Re: [Freesurfer] mris_anatomical_stats lgi error

2014-05-16 Thread _andreia_ 
Hello,

Only after sending the email below I noticed that now the stats file  
generated give only 0,00 were the LGI values should be, even though  
they appear in the terminal.

How can I solve this issue? And, again, are all the measures (cortical  
thickness, surface area, aseg) invalidated? As well as qcache? In sum,  
should I run this subject all from scratch?

Thank you in advance,
Andreia Pereira


Quoting _andre...@sapo.pt:

> Hi Doug,
>
> I tried to load the annotation and it gave an error. I look in the
> archives and I found someone with the same problem and the advice was
> to run:
>
> recon-all -s  -sd  -make all
>
> I did that and tried to run again mris_anatomical_stats as previously
> and still have this warning
>
>
> subj/stats/lh.aparc_lgi.stats subj lh
> computing statistics for each annotation in aparc.annot.
> using thickness file pial_lgi.
> reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
> reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
> reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial...
> reading input white surface  
> /home/user/visao/Freesurfer//subj/surf/lh.white...
> MRISreadNewCurvature: incompatible vertex number in file
> /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
> No such file or directory
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> structure is "bankssts"
> number of vertices  = 1160
> total surface area  = 813 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.116
> average integrated rectified Gaussian curvature = 0.031
> folding index   = 10
> intrinsic curvature index   = 1.3
> structure is "caudalanteriorcingulate"
> number of vertices  = 810
> total surface area  = 547 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.129
> average integrated rectified Gaussian curvature = 0.034
> folding index   =  9
> intrinsic curvature index   = 1.2
> structure is "caudalmiddlefrontal"
> number of vertices  = 4752
> total surface area  = 3134 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.123
> average integrated rectified Gaussian curvature = 0.033
> folding index   = 48
> intrinsic curvature index   = 6.1
> structure is "cuneus"
> number of vertices  = 2701
> total surface area  = 1667 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.164
> average integrated rectified Gaussian curvature = 0.061
> folding index   = 50
> intrinsic curvature index   = 7.1
>
> (...)
>
>
> The LGI values are generated and they seem to be in the normal range
> as all the others... I would like to know if this problem invalidates
> all the other measures that I extracted (cortical thickness and
> surface area from aparc and Brodmann areas, aseg stats)
>
> Andreia
>
>
> Quoting Douglas N Greve :
>
>> That probably means that the subject is out of synch. Try viewing the
>> subject's surface tksurfer or freeview and load the annotation.
>> doug
>>
>> On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
>>>
>>> Hello all,
>>>
>>> I generated the lgi.stats file for all my subjects and in one of them
>>> I got this warning:
>>>
>>> mris_anatomical_stats -a aparc.annot -t pial_lgi -f
>>> SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
>>> computing statistics for each annotation in aparc.annot.
>>> using thickness file pial_lgi.
>>> reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz...
>>> reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>>> reading input pial surface
>>> /home/user/visao/Freesurfer//SUBJ/surf/lh.pial...
>>> reading input white surface
>>> /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>>> *MRISreadAnnotationIntoArray: vertex index out of range: 150843
>>> i=007D324B, in_array_size=150843
>>> annot file:
>>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot*
>>> MRISreadAnnotationIntoArray: vertex index out of range: 150844
>>> i=007D324B, in_array_size=150843
>>> annot file:
>>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
>>> MRISreadAnnotationIntoArray: vertex index out of range: 150845
>>> i=007D324B, in_array_size=150843

[Freesurfer] Instruction Guide for Building FreeSurfer on Mac OSX Platforms

2014-05-16 Thread Z K 
Hello,

I have created an instruction guide for building freesurfer on OSX 
platforms. This guide is applicable for OSX 10.6, 10.7, and 10.8. 
Unfortunately I have not yet been able to successfully build on the 
latest version of OSX (Mavericks) due to changes in the most recent 
version of the gcc compiler. I will update the guide once I get that 
working.

https://freesurfer.net/fswiki/freesurfer_mac_developers_page

Please feel free to contact me with any questions or to provide any 
feedback on how to make the instruction set more complete and/or easy to 
understand.

Luke,

Getting openmp to work with the Mac build would probably require either 
modifying the "OpenMP" section of the configure.in script to check for 
gcc 4.2 (instead of 4.4) or simply using gcc 4.4 or greater on the Mac. 
I have not tried enabling openmp on the mac build yet so I cant be any 
more specific than that.

-Zeke

On 05/05/2014 05:48 PM, Z K wrote:
> I do not have any information to give in regards to when a new release
> would be available. Compiling freesurfer from source is not exactly
> something I would call "fun". That said, I have been working on a brief
> "how-to-guide" on how to build freesurfer on Mac OSX and I have already
> packaged the 3rd party libraries into a single bundle.
>
> I plan on releasing this guide next week and I will email it to you.
> Once you have it, compiling should be fairly straight forward.
>
> If you dont hear from me by next week feel free to ping me.
>
> -Zeke
>
>
>
>
> On 05/05/2014 03:59 PM, lukas.sch...@ukb.uni-bonn.de wrote:
>> Hi Zeke!
>>
>> Thanks a lot for the response. Better a late response than none :o)!
>> Do you have any vague estimate when a new release will be available?
>> So far I did not try to compile it from the sources, because it is not my
>> daily business and for an inexperienced it most likely ends up with pure
>> frustration.
>> If a new release would be close, I would definitely keep my fingers from
>> compiling ...
>> Or are any "how to's" available for compiling FS from the sources...?
>>
>> Best wishes,
>>
>> Luke
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
> ___
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>
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] mri_convert frame error in tracula

2014-05-16 Thread Pedro Rosa 
Dear All,  
As suggest, I am reposting a previous question.
I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, 
for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ 
with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is 
bval.bval and bvec.bvec.
I attached the trac-all.log that comes with the following error: ERROR: 
fMRIframe: frame >= frames

Can anyone help me?
Thank you in advance!
Regards,
Pedro Rosa.



trac-all.log
Description: Binary data
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

2014-05-16 Thread Douglas N Greve 

btw, you are strongly encouraged NOT to use FS 5.2. For TRACULA it is 
probably fine, but we found some small but systematic problems with the 
anatomical analysis in 5.2
doug

On 05/16/2014 11:51 AM, McGinnity, Colm wrote:
> Hi Anastasia,
>
> Many thanks for your help.
> I did reply but don't see the email on the forum.
>
> I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit 
> confused - I've created a 3-column bvecs format file (I had been using for 
> version 5.2.0).
>
> After running several I've noticed the 'bvecs' file in the dmri folder is 
> slightly different from the input file, whereas the 'bvecs.norot' file 
> matches the input file extactly.
>
> For example:
> File 2:
> 0.9200842 0.3251221 0.2185593 
> File 2:
> 0.919 0.3311 0.2141
>
> Can you please clarify which is used, and if these differences can be ignored?
>
> Thanks and best wishes,
> Colm.
>
>
> -Original Message-
> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
> Sent: 11 March 2014 00:39
> To: McGinnity, Colm
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
>
>
> Hi Colm - Note that the information in the tutorial (particularly the part 
> where gradient tables can be formatted in 3 rows or 3 columns) pertains to 
> the latest tracula update:
>   http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
>
> You're using an older version that only supports the 3-column format. I have 
> no idea if this is what's causing the error without looking at your 
> trac-all.log, but this would be a first guess.
>
> a.y
>
> On Mon, 10 Mar 2014, McGinnity, Colm wrote:
>
>> Dear Experts,
>>   
>> I am very new to TRACULA, I apologise for what is probably a silly question.
>>   
>> I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):
>>   
>> awk: cmd. line:1: fatal: cannot open file `0' for reading (No such
>> file or
>> directory)
>> mri_concat --i
>> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>> --mean --o /home/k1193186/
>> FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
>> niiRead(): error opening file /home/k1193186/
>> FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>> ninputs = 1
>> Checking inputs
>> ERROR: reading
>> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>>   
>> Can anyone tell me what this means and how to fix this, please?
>> I’m guessing I’ve set up my configuration wrong or have the files in
>> the wrong place?
>>   
>> Many thanks!
>> Best wishes,
>> Colm.
>> King's College London
>>   
>>   
>>   
>>
>>
>
> The information in this e-mail is intended only for the person to whom it is 
> addressed. If you believe this e-mail was sent to you in error and the e-mail 
> contains patient information, please contact the Partners Compliance HelpLine 
> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error but does not contain patient information, please contact the sender and 
> properly dispose of the e-mail.
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing

2014-05-16 Thread Douglas Merkitch 
Dear Martin and FreeSurfer experts,

Thanks for your response.

I have just finished re-running some subjects from scratch in 5.3 and it 
appears that the edits from brain.finalsurfs.manedit.mgz are not being applied 
to the longitudinal subject directories.

Just to clarify, I have been doing ALL of the pial surface edits in the 
brain.finalsurfs.manedit.mgz, not just the pial surface edits that have 
extended into the cerebellum. The rationale for doing this is mainly 
continuity, as the previous research assistant made all pial surface edits in 
this way because of a response she had received from the FS forum saying that 
there shouldn't be any problem with performing all the pial surface edits in 
the brain.finalsurfs.manedit.mgz file.

Is there something in the FreeSurfer longitudinal processing code that would 
treat edits near the cerebellum of the brain.finalsurfs.manedit.mgz file 
differently from those made in other parts of the brain (e.g. 
lateralorbitofrontal, dura, etc.,)?

Can you think of anything else that would be causing this or anything that I 
could try to get the longitudinal processing stream to incorporate the edits 
from the brain.finalsurfs.manedit.mgz file?

Thanks for your help!

Doug Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu




Begin forwarded message:

From: Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & 
longitudinal processing
Date: May 2, 2014 4:20:17 PM CDT
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Hi Doug,

so you
1. edited the cross sectionals and surfaces look fine (make sure you edit the 
brain.finalsurfs.manedit.mgz file, which you create as a copy of the 
brain.finalsurfs.mgz)
2. checked/edited the base and surfaces look fine too
3. ran the longitudinal from scratch (w/o any edits)

and then in the long, the surface looks not good?

Edits should automatically be copied from cross->long (if the manedit file 
exist). Surfaces are taken from the base to initialize longitudinal processing. 
That is why both step1 and step2 above are important. Step3 is a good idea to 
make sure that the longs are not polluted by some earlier edits. For example 
edits from cross are only copied over if the long has no manedit file, else 
only the edits in the long will be used. (I think this also answers some of the 
questions in the archive mail 1 you cite below, the archive mail 2 is a 
question about cross sectional processing, but I think there the problem is 
that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so 
edits probably get overwritten).

I also have the feeling that we fixed something about the editing in 
longitudinal processing after 5.1, but cannot find it documented on the wiki 
(so not sure). You may want to try to run this with 5.3 if it does not work 
with 5.1

Best, Martin


On 05/02/2014 10:45 AM, Douglas Merkitch wrote:
Dear Freesurfer experts,

I have a question regarding longitudinal edits. Specifically the 
brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in 
Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525).

The problem that I am having is that the edits saved in the 
brain.finalsurfs.manedit.mgz file do not carry over when processing 
longitudinally.

Previous posts have addressed this topic, but have not (to my knowledge) solved 
the issue. Please see the threads from the Freesurfer archive below for a brief 
context:

1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html

2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html

Please let me know if more information is needed to understand the issue.

Any insight/ideas regarding this issue would be greatly appreciated!

Thanks,

Doug

Doug Merkitch
Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: douglas_merki...@rush.edu






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--
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.ed

Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

2014-05-16 Thread McGinnity, Colm 
Hi Anastasia,

Thanks for your reply. 
Oh, of course, sorry I didn't realise I was looking at the bvecs after the 
rotation. Now it makes sense.

Best wishes,
Colm.


> On 16 May 2014, at 16:59, "Anastasia Yendiki"  
> wrote:
> 
> 
> Hi Colm - The final version used is bvecs. The eddy current correction step 
> registers each DWI to the first b=0 image, and the same transformation is 
> applied to the corresponding gradient vector. This is a standard procedure 
> when doing eddy current correction by registration.
> 
> Hope this helps,
> a.y
> 
>> On Fri, 16 May 2014, McGinnity, Colm wrote:
>> 
>> Hi Anastasia,
>> 
>> Many thanks for your help.
>> I did reply but don't see the email on the forum.
>> 
>> I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit 
>> confused - I've created a 3-column bvecs format file (I had been using for 
>> version 5.2.0).
>> 
>> After running several I've noticed the 'bvecs' file in the dmri folder is 
>> slightly different from the input file, whereas the 'bvecs.norot' file 
>> matches the input file extactly.
>> 
>> For example:
>> File 2:
>> 0.9200842 0.3251221 0.2185593
>> File 2:
>> 0.9190.3311 0.2141
>> 
>> Can you please clarify which is used, and if these differences can be 
>> ignored?
>> 
>> Thanks and best wishes,
>> Colm.
>> 
>> 
>> -Original Message-
>> From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
>> Sent: 11 March 2014 00:39
>> To: McGinnity, Colm
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
>> 
>> 
>> Hi Colm - Note that the information in the tutorial (particularly the part 
>> where gradient tables can be formatted in 3 rows or 3 columns) pertains to 
>> the latest tracula update:
>>http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
>> 
>> You're using an older version that only supports the 3-column format. I have 
>> no idea if this is what's causing the error without looking at your 
>> trac-all.log, but this would be a first guess.
>> 
>> a.y
>> 
>>> On Mon, 10 Mar 2014, McGinnity, Colm wrote:
>>> 
>>> Dear Experts,
>>>  
>>> I am very new to TRACULA, I apologise for what is probably a silly question.
>>>  
>>> I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):
>>>  
>>> awk: cmd. line:1: fatal: cannot open file `0' for reading (No such
>>> file or
>>> directory)
>>> mri_concat --i
>>> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>>> --mean --o /home/k1193186/
>>> FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
>>> niiRead(): error opening file /home/k1193186/
>>> FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>>> ninputs = 1
>>> Checking inputs
>>> ERROR: reading
>>> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>>>  
>>> Can anyone tell me what this means and how to fix this, please?
>>> I’m guessing I’ve set up my configuration wrong or have the files in
>>> the wrong place?
>>>  
>>> Many thanks!
>>> Best wishes,
>>> Colm.
>>> King's College London
>> 
>> 
>> The information in this e-mail is intended only for the person to whom it is 
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail contains patient information, please contact the Partners Compliance 
>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent 
>> to you in error but does not contain patient information, please contact the 
>> sender and properly dispose of the e-mail.
>> 
>> 

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Re: [Freesurfer] Setup and configuration problem ubuntu 12.04.LTS

2014-05-16 Thread Z K 
Hello Alejandra,

I've seen this error before when people have tried to run freesurfer on 
cluster machines. The error indicates that the necessary X-libs are not 
installed. Google tells me that if you or your sys admin can install 
libXScrnSaver onto your machine it *should* fix it.

Best,
-Zeke

On 05/16/2014 10:26 AM, Alejandra Machado wrote:
> Hello,
>
> i'm trying to setup freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.
>
> I think i've done downloading properly but i'm having some trouble with
> installation. I can set up enviroment and when testing freesurfer with
> some of the scripts from the page, sometimes it works but sometimes i
> get an error.
>
> Can you please help me?
>
> Thank you!
> Alejandra
>
>
> Ale:~> setenv FREESURFER_HOME /usr/local/freesurfer
> Ale:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>  freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer
> FSFAST_HOME   /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/freesurfer/subjects
> MNI_DIR   /usr/local/freesurfer/mni
> Ale:~> freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
> freeview.bin: error while loading shared libraries: libXss.so.1: cannot
> open shared object file: No such file or directory
> Ale:~>
> tkmedit bert orig.mgz
> Reading /usr/local/freesurfer/tktools/tkm_common.tcl
> Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/tktools/tkUtils.tcl
> % Ale:~> freeview
> freeview.bin: error while loading shared libraries: libXss.so.1: cannot
> open shared object file: No such file or directory
> Ale:~> qdec
> qdec.bin: error while loading shared libraries: libXss.so.1: cannot open
> shared object file: No such file or directory
> Ale:~>
>
>
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Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

2014-05-16 Thread Anastasia Yendiki 


Hi Colm - The final version used is bvecs. The eddy current correction 
step registers each DWI to the first b=0 image, and the same 
transformation is applied to the corresponding gradient vector. This is a 
standard procedure when doing eddy current correction by registration.


Hope this helps,
a.y

On Fri, 16 May 2014, McGinnity, Colm wrote:


Hi Anastasia,

Many thanks for your help.
I did reply but don't see the email on the forum.

I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit 
confused - I've created a 3-column bvecs format file (I had been using for 
version 5.2.0).

After running several I've noticed the 'bvecs' file in the dmri folder is 
slightly different from the input file, whereas the 'bvecs.norot' file matches 
the input file extactly.

For example:
File 2:
0.9200842 0.3251221 0.2185593
File 2:
0.919   0.3311 0.2141

Can you please clarify which is used, and if these differences can be ignored?

Thanks and best wishes,
Colm.


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0


Hi Colm - Note that the information in the tutorial (particularly the part 
where gradient tables can be formatted in 3 rows or 3 columns) pertains to the 
latest tracula update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

You're using an older version that only supports the 3-column format. I have no 
idea if this is what's causing the error without looking at your trac-all.log, 
but this would be a first guess.

a.y

On Mon, 10 Mar 2014, McGinnity, Colm wrote:


Dear Experts,
 
I am very new to TRACULA, I apologise for what is probably a silly question.
 
I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):
 
awk: cmd. line:1: fatal: cannot open file `0' for reading (No such
file or
directory)
mri_concat --i
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
--mean --o /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
niiRead(): error opening file /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
 
Can anyone tell me what this means and how to fix this, please?
I’m guessing I’ve set up my configuration wrong or have the files in
the wrong place?
 
Many thanks!
Best wishes,
Colm.
King's College London
 
 
 





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Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

2014-05-16 Thread McGinnity, Colm 
Hi Anastasia,

Many thanks for your help.
I did reply but don't see the email on the forum. 

I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit 
confused - I've created a 3-column bvecs format file (I had been using for 
version 5.2.0). 

After running several I've noticed the 'bvecs' file in the dmri folder is 
slightly different from the input file, whereas the 'bvecs.norot' file matches 
the input file extactly. 

For example: 
File 2:
0.9200842 0.3251221 0.2185593   
File 2:
0.919   0.3311 0.2141

Can you please clarify which is used, and if these differences can be ignored?

Thanks and best wishes,
Colm.


-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] 
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0


Hi Colm - Note that the information in the tutorial (particularly the part 
where gradient tables can be formatted in 3 rows or 3 columns) pertains to the 
latest tracula update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

You're using an older version that only supports the 3-column format. I have no 
idea if this is what's causing the error without looking at your trac-all.log, 
but this would be a first guess.

a.y

On Mon, 10 Mar 2014, McGinnity, Colm wrote:

> Dear Experts,
>  
> I am very new to TRACULA, I apologise for what is probably a silly question.
>  
> I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):
>  
> awk: cmd. line:1: fatal: cannot open file `0' for reading (No such 
> file or
> directory)
> mri_concat --i
> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz 
> --mean --o /home/k1193186/ 
> FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
> niiRead(): error opening file /home/k1193186/ 
> FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
> ninputs = 1
> Checking inputs
> ERROR: reading
> /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
>  
> Can anyone tell me what this means and how to fix this, please?
> I’m guessing I’ve set up my configuration wrong or have the files in 
> the wrong place?
>  
> Many thanks!
> Best wishes,
> Colm.
> King's College London
>  
>  
>  
> 
>


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contains patient information, please contact the Partners Compliance HelpLine 
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[Freesurfer] Setup and configuration problem ubuntu 12.04.LTS

2014-05-16 Thread Alejandra Machado 
Hello,

i'm trying to setup freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.

I think i've done downloading properly but i'm having some trouble with
installation. I can set up enviroment and when testing freesurfer with some
of the scripts from the page, sometimes it works but sometimes i get an
error.

Can you please help me?

Thank you!
Alejandra


Ale:~> setenv FREESURFER_HOME /usr/local/freesurfer
Ale:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
Ale:~> freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
Ale:~>
tkmedit bert orig.mgz
Reading /usr/local/freesurfer/tktools/tkm_common.tcl
Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/tktools/tkUtils.tcl
% Ale:~> freeview
freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
Ale:~> qdec
qdec.bin: error while loading shared libraries: libXss.so.1: cannot open
shared object file: No such file or directory
Ale:~>
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Re: [Freesurfer] Tracula - configuration file error

2014-05-16 Thread ayendiki 
Hi Pedro - Looks like the mri_convert command has trouble reading your
dicoms. Have you searched for that error message in the archives of the
freesurfer list? If nobody has encountered it before, then you can post
this as an mri_convert question so that the appropriate people look at it.

a.y

> Hi,
> Thank you a lot! It now ran, but exited with errors: ERROR: fMRIframe:
> frame >= n frames
> Can you help me?
> Regards,
> Pedro Rosa
>
> [server:~/Desktop] pedrogomesrosa% trac-all -corr -c config
> INFO: SUBJECTS_DIR is /Users/pedrogomesrosa/Desktop
> INFO: Diffusion root is /Users/pedrogomesrosa/Desktop
> Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer
> INFO: current FREESURFER_HOME does not match that of previous processing.
> Current: /Applications/Freesurfer5.3/freesurfer
> Previous: /Volumes/Data/Freesurfer_5.3/freesurfer
> trac-preproc -c /Users/pedrogomesrosa/Desktop/ESNA148/scripts/dmrirc.local
> -log /Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.log -cmd
> /Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.cmd
> #-
> /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc
> #-
> #@# Image corrections Fri May 16 08:35:20 BRT 2014
> mri_convert
> /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm
> /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz
> mri_convert
> /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm
> /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
> /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm...
> Getting Series No
> INFO: Found 6612 files in /Users/pedrogomesrosa/Desktop//148
> INFO: Scanning for Series Number 5
> Scanning Directory
> INFO: found 6501 files in series
> INFO: loading series header info.
> error:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings:
> can't open file:
> /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808391678947142928
> (No such file or directory)
> error:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings:
> can't open file: copy.dcm (No such file or directory)
>
> RunNo = 4
> WARNING: Run 4 appears to be truncated
>   Slice = 1, nthframe = 1, nframes = 2, 0
> INFO: sorting.
> INFO: (120 120   1), nframes = 2, ismosaic=0
> PE Dir COL COL
> AutoAlign matrix detected
> AutoAlign Matrix -
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
>
> ERROR: nlist (6501) > nslices (1) x frames (2)
> ERROR: dump file list into fileinfo.txt.
> ERROR: check for consistency
> ERROR: set nlist = nslices*nframes.
> FileName
> /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808214939782717907.dcm
> Identification
> NumarisVersyngo MR B15
> ScannerModel  Espree
> PatientName   RODRIGUES^ADRIANA C
> Date and time
> StudyDate 20121128
> StudyTime 075625.593000
> SeriesTime082207.781000
> AcqTime   082147.882500
> Acquisition parameters
> PulseSeq  *ep_b0
> Protocol  DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro)
> PhEncDir  COL
> EchoNo1
> FlipAngle 90
> EchoTime  110
> InversionTime -1
> RepetitionTime8000
> PhEncFOV  240
> ReadoutFOV240
> Image information
> RunNo 4
> SeriesNo  5
> ImageNo   1
> NImageRows120
> NImageCols120
> NFrames   2
> SliceArraylSize   50
> IsMosaic  0
> ImgPos120.1304  78.5600 -52.6158
> VolRes  2.   2.   2.7000
> VolDim120  1201
> Vc -1.  -0.   0.
> Vr -0.  -1.   0.
> Vs -0.  -0.   1.
> VolCenter   0.1304 -41.4400 -51.2658
> TransferSyntaxUID 1.2.840.10008.1.2.1
> UseSliceScaleFactor 0 (slice 0: 1)
> INFO: no Siemens slice order reversal detected (good!).
> TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00
> i_ras = (-1, -0, 0)
> j_ras = (-0, -1, 0)
> k_ras = (-0, -0, 1)
> writing to /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz...
> mri_probedicom --i
> /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm
> > /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dcminfo.dat
> cp /Users/pedrogomesrosa/Desktop/bvec.bvec
> /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs
> cp /Users/pedrogomesrosa/Desktop/bval.bval
> /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals
> mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvecs.tmp
> /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs
> mv -f /Use

[Freesurfer] Small volume correction in qdec

2014-05-16 Thread Narly Golestani 

Dear all,

I would like to follow up on several posts that have already been made 
regarding how to restrict the search volume (i.e. do a small volume correction) 
to a particular region (e.g. to a freesurfer label) within qdec.  As far as I 
can see this query was not answered on the list: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13770.html

How exactly can this be implemented in qdec please?

Thanks in advance and best wishes,
Narly.
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Re: [Freesurfer] Tracula - configuration file error

2014-05-16 Thread Pedro Rosa 
Hi,  
Thank you a lot! It now ran, but exited with errors: ERROR: fMRIframe: frame >= 
n frames
Can you help me?
Regards,
Pedro Rosa

[server:~/Desktop] pedrogomesrosa% trac-all -corr -c config  
INFO: SUBJECTS_DIR is /Users/pedrogomesrosa/Desktop
INFO: Diffusion root is /Users/pedrogomesrosa/Desktop
Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/Freesurfer5.3/freesurfer
Previous: /Volumes/Data/Freesurfer_5.3/freesurfer
trac-preproc -c /Users/pedrogomesrosa/Desktop/ESNA148/scripts/dmrirc.local -log 
/Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.log -cmd 
/Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.cmd
#-
/Applications/Freesurfer5.3/freesurfer/bin/trac-preproc  
#-
#@# Image corrections Fri May 16 08:35:20 BRT 2014
mri_convert 
/Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm
 /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz
mri_convert 
/Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm
 /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz  
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm...
Getting Series No  
INFO: Found 6612 files in /Users/pedrogomesrosa/Desktop//148
INFO: Scanning for Series Number 5
Scanning Directory  
INFO: found 6501 files in series
INFO: loading series header info.
error: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings:
 can't open file: 
/Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808391678947142928
 (No such file or directory)
error: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings:
 can't open file: copy.dcm (No such file or directory)

RunNo = 4  
WARNING: Run 4 appears to be truncated
  Slice = 1, nthframe = 1, nframes = 2, 0
INFO: sorting.
INFO: (120 120   1), nframes = 2, ismosaic=0
PE Dir COL COL
AutoAlign matrix detected  
AutoAlign Matrix -  
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

ERROR: nlist (6501) > nslices (1) x frames (2)  
ERROR: dump file list into fileinfo.txt.
ERROR: check for consistency
ERROR: set nlist = nslices*nframes.
FileName 
/Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808214939782717907.dcm
Identification
NumarisVersyngo MR B15
ScannerModel  Espree
PatientName   RODRIGUES^ADRIANA C  
Date and time
StudyDate 20121128
StudyTime 075625.593000  
SeriesTime082207.781000  
AcqTime   082147.882500  
Acquisition parameters
PulseSeq  *ep_b0
Protocol  DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro)  
PhEncDir  COL
EchoNo1
FlipAngle 90
EchoTime  110
InversionTime -1
RepetitionTime8000
PhEncFOV  240
ReadoutFOV240
Image information
RunNo 4
SeriesNo  5
ImageNo   1
NImageRows120
NImageCols120
NFrames   2
SliceArraylSize   50
IsMosaic  0
ImgPos120.1304  78.5600 -52.6158  
VolRes  2.   2.   2.7000  
VolDim120  1201  
Vc -1.  -0.   0.  
Vr -0.  -1.   0.  
Vs -0.  -0.   1.  
VolCenter   0.1304 -41.4400 -51.2658  
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).  
TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz...
mri_probedicom --i 
/Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm
 > /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dcminfo.dat
cp /Users/pedrogomesrosa/Desktop/bvec.bvec 
/Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs
cp /Users/pedrogomesrosa/Desktop/bval.bval 
/Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals
mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvecs.tmp 
/Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs
mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvals.tmp 
/Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals
flip4fsl /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz 
/Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 10.8
fslswapdim /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz x -y z 
/Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.g

Re: [Freesurfer] Tracula - configuration file error

2014-05-16 Thread ayendiki 
Hi Pedro - Your config file needs to be a plain text file, not a rich text
format (rtf) file. If you run the cat command on your file, you'll see
that there are some formatting strings that were added by your text editor
in the beginning of the file and they include the curly brackets that give
you the error.

Hope this helps,
a.y

> Dear all,
> I am facing an error at the configuration file for trac-all
> I am trying to run a single subject, 148, for who there is a folder
> ‘148’ with all DWI DICOMs and a folder ‘ESNA148’ with the
> recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is
> bval.bval and bvec.bvec.
> I attached the configuration file.
> However, I am facing the following error, although no run list is
> specified:
> [server:~/Desktop] pedrogomesrosa% trac-all -corr -c config.rtf
> Missing }.
> Missing }.
> }: Command not found.
> Missing }.
> red255green255blue255: Command not found.
> red240green242blue245: Command not found.
> }: Command not found.
> margl1440margr1440vieww22600viewh9020viewkind0: Command not found.
> deftab720: Command not found.
> pardpardeftab720: Command not found.
> ERROR: run list is longer than subject list
>
>
> Any input is appreciated.
> Regards,
> Pedro Rosa.
>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mris_anatomical_stats lgi error

2014-05-16 Thread _andreia_ 
Hi Doug,

I tried to load the annotation and it gave an error. I look in the  
archives and I found someone with the same problem and the advice was  
to run:

recon-all -s  -sd  -make all

I did that and tried to run again mris_anatomical_stats as previously  
and still have this warning


subj/stats/lh.aparc_lgi.stats subj lh
computing statistics for each annotation in aparc.annot.
using thickness file pial_lgi.
reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial...
reading input white surface /home/user/visao/Freesurfer//subj/surf/lh.white...
MRISreadNewCurvature: incompatible vertex number in file  
/home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
No such file or directory
reading colortable from annotation file...
colortable with 36 entries read (originally  
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
structure is "bankssts"
number of vertices  = 1160
total surface area  = 813 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.116
average integrated rectified Gaussian curvature = 0.031
folding index   = 10
intrinsic curvature index   = 1.3
structure is "caudalanteriorcingulate"
number of vertices  = 810
total surface area  = 547 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.129
average integrated rectified Gaussian curvature = 0.034
folding index   =  9
intrinsic curvature index   = 1.2
structure is "caudalmiddlefrontal"
number of vertices  = 4752
total surface area  = 3134 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.123
average integrated rectified Gaussian curvature = 0.033
folding index   = 48
intrinsic curvature index   = 6.1
structure is "cuneus"
number of vertices  = 2701
total surface area  = 1667 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.164
average integrated rectified Gaussian curvature = 0.061
folding index   = 50
intrinsic curvature index   = 7.1

(...)


The LGI values are generated and they seem to be in the normal range  
as all the others... I would like to know if this problem invalidates  
all the other measures that I extracted (cortical thickness and  
surface area from aparc and Brodmann areas, aseg stats)

Andreia


Quoting Douglas N Greve :

> That probably means that the subject is out of synch. Try viewing the
> subject's surface tksurfer or freeview and load the annotation.
> doug
>
> On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
>>
>> Hello all,
>>
>> I generated the lgi.stats file for all my subjects and in one of them
>> I got this warning:
>>
>> mris_anatomical_stats -a aparc.annot -t pial_lgi -f
>> SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
>> computing statistics for each annotation in aparc.annot.
>> using thickness file pial_lgi.
>> reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz...
>> reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>> reading input pial surface
>> /home/user/visao/Freesurfer//SUBJ/surf/lh.pial...
>> reading input white surface
>> /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>> *MRISreadAnnotationIntoArray: vertex index out of range: 150843
>> i=007D324B, in_array_size=150843
>> annot file:
>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot*
>> MRISreadAnnotationIntoArray: vertex index out of range: 150844
>> i=007D324B, in_array_size=150843
>> annot file:
>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
>> MRISreadAnnotationIntoArray: vertex index out of range: 150845
>> i=007D324B, in_array_size=150843
>> annot file:
>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
>>
>> (...)
>>
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>> structure is "bankssts"
>> number of vertices  = 1139
>> total surface area  = 795 mm^2
>> total gray matter volume= 2868 mm^3
>> average cortical thickness  = 3.820 mm +- 0.158 mm
>> average integrated rectified mean curvature = 0.11